Introduction

sanger-tol/genealignment is a bioinformatics pipeline that generated geneset alignments to a specified input genome. This pipeline will be used for evaluating genesets for use in TreeVal

1. YAML_INPUT -- Parses the input yaml into Channels for downstream use.
2. GENERATE_GENOME -- Generates a trimmed fasta index file for us in JBrowse.
3. GENE_ALIGNMENT -- Align geneset data against the input genome.

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Much of the information regarding running this pipeline can be found on the TreeVal usage page.

The input yaml should consist of the following:

assembly:
  assem_level: scaffold
  assem_version: 1
  sample_id: Oscheius_DF5033
  latin_name: to_provide_taxonomic_rank
  defined_class: nematode
  project_id: DTOL
reference_file: TOLID.fasta
alignment:
  data_dir: /path/to/gene_alignment_data/
  common_name: "" # For future implementation (adding bee, wasp, ant etc)
  geneset_id: "OscheiusTipulae.ASM1342590v1,CaenorhabditisElegans.WBcel235,Gae_host.Gae"
intron:
  size: "50k"

Now, you can run the pipeline using:

nextflow run sanger-tol/genealignment \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.yaml \
   --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

sanger-tol/genealignment was originally written by DLBPointon.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.